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Crystal structure of kluyveromyces polysporus argonaute with a guide RNA

Analyse Crystal structure of kluyveromyces polysporus argonaute with a guide RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4F1N
Type: protein + RNA
Length: 1,773 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kpago; RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'
UniProt: A7TMA9
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kpago	protein	904	30% helix, 23% strand	A7TMA9
E, F	RNA 5'-R(PUPAPAPAPAPAPAPAP*A)-3'	rna	8	—	—
B	Kpago	protein	853	31% helix, 23% strand	A7TMA9

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.74	0.83	61	empty
2	1030	0.74	0.77	73	empty
3	847	0.73	0.78	66	empty
4	683	0.66	0.75	67	empty
5	290	0.63	0.81	36	empty

Interfaces

3 interfaces between chains.

A–E · 1243 Å² buried · 31 hydrogen bonds · protein-nucleic
B–F · 1240 Å² buried · 29 hydrogen bonds · protein-nucleic
A–B · 305 Å² buried · 3 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A7TMA9
Elsewhere: RCSB PDB 4F1N · PDBe 4F1N · UniProt A7TMA9

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